SMTL ID : 7wlk.1

CryoEM structure of human low-voltage activated T-type calcium channel Cav3.3 in complex with Otilonium Bromide(OB)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x 7TB: 2-[diethyl(methyl)-$l^{4}-azanyl]ethyl 4-[(2-octoxyphenyl)carbonylamino]benzoate(Non-covalent)

7TB.1: 14 residues within 4Å: Chain A: N.391, M.759, C.766, F.815, L.818, T.819, Q.820, N.850, F.854, K.1379, L.1416, S.1419, F.1426 Ligands: 3PE.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.815, A:L.818, A:T.819, A:F.854, A:F.854, A:F.854, A:L.1416 Hydrogen bonds: A:L.818, A:Q.820, A:K.1379, A:S.1419 pi-Cation interactions: A:K.1379

6 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)(Non-functional Binders)

3PE.2: 16 residues within 4Å: Chain A: L.1303, V.1310, C.1313, F.1374, A.1377, S.1378, K.1379, V.1422, M.1425, T.1716, Q.1718, F.1719, I.1722 Ligands: 7TB.1, 3PE.3, Y01.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.1303, A:V.1310, A:F.1374, A:T.1716, A:Q.1718, A:F.1719, A:I.1722 Salt bridges: A:K.1379 3PE.3: 7 residues within 4Å: Chain A: L.356, F.387, F.1672, S.1675, Q.1718, L.1721 Ligands: 3PE.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.356, A:F.387, A:F.1672, A:L.1721 3PE.5: 2 residues within 4Å: Chain A: F.1495, C.1498 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1495 3PE.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 3PE.7: 2 residues within 4Å: Chain A: N.1404 Ligands: 3PE.15 No protein-ligand interaction detected (PLIP) 3PE.15: 5 residues within 4Å: Chain A: V.729, T.732, F.733, L.736 Ligands: 3PE.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.729, A:F.733, A:L.736

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.357, E.821, D.1380 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.357, A:D.1380 CA.17: 4 residues within 4Å: Chain A: E.357, Q.820, K.1379, G.1677 No protein-ligand interaction detected (PLIP)

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)(Covalent)

Y01.8: 10 residues within 4Å: Chain A: F.223, I.226, L.230, N.275, H.370, S.371, Y.373, N.374, Y.377, V.384 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.226, A:I.226, A:L.230, A:Y.373, A:Y.377, A:V.384 Salt bridges: A:H.370 Y01.9: 7 residues within 4Å: Chain A: T.654, G.658, I.659, H.661, N.1365, L.1366 Ligands: Y01.10 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.654, A:I.659, A:N.1365, A:L.1366, A:L.1366, A:L.1366 Salt bridges: A:H.661 Y01.10: 9 residues within 4Å: Chain A: C.1314, G.1367, Q.1368, L.1370, F.1374, Q.1703, F.1704 Ligands: 3PE.2, Y01.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.1370, A:F.1704 Y01.12: 8 residues within 4Å: Chain A: L.779, I.783, T.834, S.835, W.837, A.838, L.840, Y.841 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.779, A:I.783, A:A.838, A:L.840 Y01.14: 8 residues within 4Å: Chain A: F.372, F.375, I.379, M.1666, F.1668, L.1669, F.1672 Ligands: Y01.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.372, A:F.375, A:I.379, A:F.1668, A:F.1668, A:F.1672 Y01.16: 8 residues within 4Å: Chain A: F.1181, I.1185, A.1188, L.1189, R.1191, N.1663, F.1664 Ligands: Y01.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.1181, A:I.1185, A:A.1188, A:N.1663, A:F.1664 Salt bridges: A:R.1191

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.11: 3 residues within 4Å: Chain A: N.1345, S.1347, D.1348 No protein-ligand interaction detected (PLIP) NAG.13: 3 residues within 4Å: Chain A: D.1339, R.1341, N.1342 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, L. et al., Structure, gating, and pharmacology of human Ca V 3.3 channel. Nat Commun (2022)

Release Date

2022-05-04

Peptides

Voltage-dependent T-type calcium channel subunit alpha-1I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent T-type calcium channel subunit alpha-1I

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